OpenRaiser/Intern-Atlas huggingface dataset:
Prediction by Machine Learning Analysis of Genomic Data Phenotypic Frost Tolerance in Perccottus glenii
Venue: arXiv cs.LG 2024
Year: 2024

Analysis of the genome sequence of Perccottus glenii, the only fish known to possess freeze tolerance, holds significant importance for understanding how organisms adapt to extreme environments, Traditional biological analysis methods are time-consuming and have limited accuracy, To address these issues, we will employ machine learning techniques to analyze the gene sequences of Perccottus glenii, with Neodontobutis hainanens as a comparative group, Firstly, we have proposed five gene sequence vectorization methods and a method for handling ultra-long gene sequences, We conducted a comparative study on the three vectorization methods: ordinal encoding, One-Hot encoding, and K-mer encoding, to identify the optimal encoding method, Secondly, we constructed four classification models: Random Forest, LightGBM, XGBoost, and Decision Tree, The dataset used by these classification models was extracted from the National Center for Biotechnology Information database, and we vectorized the sequence matrices using the optimal encoding method, K-mer, The Random Forest model, which is the optimal model, achieved a classification accuracy of up to 99, 98 , Lastly, we utilized SHAP values to conduct an interpretable analysis of the optimal classification model, Through ten-fold cross-validation and the AUC metric, we identified the top 10 features that contribute the most to the model's classification accuracy, This demonstrates that machine learning methods can effectively replace traditional manual analysis in identifying genes associated with the freeze tolerance phenotype in Perccottus glenii.
Evolution of SAE Features Across Layers in LLMs
Venue: arXiv cs.LG 2024
Year: 2024

Sparse Autoencoders for transformer-based language models are typically defined independently per layer. In this work we analyze statistical relationships between features in adjacent layers to understand how features evolve through a forward pass. We provide a graph visualization interface for features and their most similar next-layer neighbors (https://stefanhex.com/spar-2024/feature-browser/), and build communities of related features across layers. We find that a considerable amount of features are passed through from a previous layer, some features can be expressed as quasi-boolean combinations of previous features, and some features become more specialized in later layers.
Can we hop in general? A discussion of benchmark selection and design using the Hopper environment
Venue: arXiv cs.LG 2024
Year: 2024

Empirical, benchmark-driven testing is a fundamental paradigm in the current RL community. While using off-the-shelf benchmarks in reinforcement learning (RL) research is a common practice, this choice is rarely discussed. Benchmark choices are often done based on intuitive ideas like "legged robots" or "visual observations". In this paper, we argue that benchmarking in RL needs to be treated as a scientific discipline itself. To illustrate our point, we present a case study on different variants of the Hopper environment to show that the selection of standard benchmarking suites can drastically change how we judge performance of algorithms. The field does not have a cohesive notion of what the different Hopper environments are representative - they do not even seem to be representative of each other. Our experimental results suggests a larger issue in the deep RL literature: benchmark choices are neither commonly justified, nor does there exist a language that could be used to justify the selection of certain environments. This paper concludes with a discussion of the requirements for proper discussion and evaluations of benchmarks and recommends steps to start a dialogue towards this goal.
Experiments with Choice in Dependently-Typed Higher-Order Logic
Venue: arXiv cs.LO 2024
Year: 2024

Recently an extension to higher-order logic -- called DHOL -- was introduced, enriching the language with dependent types, and creating a powerful extensional type theory. In this paper we propose two ways how choice can be added to DHOL. We extend the DHOL term structure by Hilbert's indefinite choice operator $ε$, define a translation of the choice terms to HOL choice that extends the existing translation from DHOL to HOL and show that the extension of the translation is complete and give an argument for soundness. We finally evaluate the extended translation on a set of dependent HOL problems that require choice.
Calibrated Cache Model for Few-Shot Vision-Language Model Adaptation
Venue: arXiv cs.CV 2024
Year: 2024

Cache-based approaches stand out as both effective and efficient for adapting vision-language models (VLMs). Nonetheless, the existing cache model overlooks three crucial aspects. 1) Pre-trained VLMs are mainly optimized for image-text similarity, neglecting the importance of image-image similarity, leading to a gap between pre-training and adaptation. 2) The current cache model is based on the Nadaraya-Watson (N-W) estimator, which disregards the intricate relationships among training samples while constructing weight function. 3) Under the condition of limited samples, the logits generated by cache model are of high uncertainty, directly using these logits without accounting for the confidence could be problematic. This work presents three calibration modules aimed at addressing the above challenges. Similarity Calibration refines the image-image similarity by using unlabeled images. We add a learnable projection layer with residual connection on top of the pre-trained image encoder of CLIP and optimize the parameters by minimizing self-supervised contrastive loss. Weight Calibration introduces a precision matrix into the weight function to adequately model the relation between training samples, transforming the existing cache model to a Gaussian Process (GP) regressor, which could be more accurate than N-W estimator. Confidence Calibration leverages the predictive variances computed by GP Regression to dynamically re-scale the logits of cache model, ensuring that the cache model's outputs are appropriately adjusted based on their confidence levels. Besides, to reduce the high complexity of GPs, we further propose a group-based learning strategy. Integrating the above designs, we propose both training-free and training-required variants. Extensive experiments on 11 few-shot classification datasets validate that the proposed methods can achieve state-of-the-art performance.
Path-minimizing Latent ODEs for improved extrapolation and inference
Venue: arXiv cs.LG 2024
Year: 2024

Latent ODE models provide flexible descriptions of dynamic systems, but they can struggle with extrapolation and predicting complicated non-linear dynamics. The latent ODE approach implicitly relies on encoders to identify unknown system parameters and initial conditions, whereas the evaluation times are known and directly provided to the ODE solver. This dichotomy can be exploited by encouraging time-independent latent representations. By replacing the common variational penalty in latent space with an $\ell_2$ penalty on the path length of each system, the models learn data representations that can easily be distinguished from those of systems with different configurations. This results in faster training, smaller models, more accurate interpolation and long-time extrapolation compared to the baseline ODE models with GRU, RNN, and LSTM encoder/decoders on tests with damped harmonic oscillator, self-gravitating fluid, and predator-prey systems. We also demonstrate superior results for simulation-based inference of the Lotka-Volterra parameters and initial conditions by using the latents as data summaries for a conditional normalizing flow. Our change to the training loss is agnostic to the specific recognition network used by the decoder and can therefore easily be adopted by other latent ODE models.
Meta-Transfer Learning Empowered Temporal Graph Networks for Cross-City Real Estate Appraisal
Venue: arXiv cs.LG 2024
Year: 2024

Real estate appraisal is important for a variety of endeavors such as real estate deals, investment analysis, and real property taxation. Recently, deep learning has shown great promise for real estate appraisal by harnessing substantial online transaction data from web platforms. Nonetheless, deep learning is data-hungry, and thus it may not be trivially applicable to enormous small cities with limited data. To this end, we propose Meta-Transfer Learning Empowered Temporal Graph Networks (MetaTransfer) to transfer valuable knowledge from multiple data-rich metropolises to the data-scarce city to improve valuation performance. Specifically, by modeling the ever-growing real estate transactions with associated residential communities as a temporal event heterogeneous graph, we first design an Event-Triggered Temporal Graph Network to model the irregular spatiotemporal correlations between evolving real estate transactions. Besides, we formulate the city-wide real estate appraisal as a multi-task dynamic graph link label prediction problem, where the valuation of each community in a city is regarded as an individual task. A Hypernetwork-Based Multi-Task Learning module is proposed to simultaneously facilitate intra-city knowledge sharing between multiple communities and task-specific parameters generation to accommodate the community-wise real estate price distribution. Furthermore, we propose a Tri-Level Optimization Based Meta- Learning framework to adaptively re-weight training transaction instances from multiple source cities to mitigate negative transfer, and thus improve the cross-city knowledge transfer effectiveness. Finally, extensive experiments based on five real-world datasets demonstrate the significant superiority of MetaTransfer compared with eleven baseline algorithms.
Evaluating Federated Kolmogorov-Arnold Networks on Non-IID Data
Venue: arXiv cs.LG 2024
Year: 2024

Federated Kolmogorov-Arnold Networks (F-KANs) have already been proposed, but their assessment is at an initial stage. We present a comparison between KANs (using B-splines and Radial Basis Functions as activation functions) and Multi- Layer Perceptrons (MLPs) with a similar number of parameters for 100 rounds of federated learning in the MNIST classification task using non-IID partitions with 100 clients. After 15 trials for each model, we show that the best accuracies achieved by MLPs can be achieved by Spline-KANs in half of the time (in rounds), with just a moderate increase in computing time.
AI versus AI in Financial Crimes and Detection: GenAI Crime Waves to Co-Evolutionary AI
Venue: arXiv cs.LG 2024
Year: 2024

Adoption of AI by criminal entities across traditional and emerging financial crime paradigms has been a disturbing recent trend. Particularly concerning is the proliferation of generative AI, which has empowered criminal activities ranging from sophisticated phishing schemes to the creation of hard-to-detect deep fakes, and to advanced spoofing attacks to biometric authentication systems. The exploitation of AI by criminal purposes continues to escalate, presenting an unprecedented challenge. AI adoption causes an increasingly complex landscape of fraud typologies intertwined with cybersecurity vulnerabilities. Overall, GenAI has a transformative effect on financial crimes and fraud. According to some estimates, GenAI will quadruple the fraud losses by 2027 with a staggering annual growth rate of over 30% [27]. As crime patterns become more intricate, personalized, and elusive, deploying effective defensive AI strategies becomes indispensable. However, several challenges hinder the necessary progress of AI-based fincrime detection systems. This paper examines the latest trends in AI/ML-driven financial crimes and detection systems. It underscores the urgent need for developing agile AI defenses that can effectively counteract the rapidly emerging threats. It also aims to highlight the need for cooperation across the financial services industry to tackle the GenAI induced crime waves.
Automating Bibliometric Analysis with Sentence Transformers and Retrieval-Augmented Generation (RAG): A Pilot Study in Semantic and Contextual Search for Customized Literature Characterization for High-Impact Urban Research
Venue: arXiv cs.DL 2024
Year: 2024

Bibliometric analysis is essential for understanding research trends, scope, and impact in urban science, especially in high-impact journals, such Nature Portfolios. However, traditional methods, relying on keyword searches and basic NLP techniques, often fail to uncover valuable insights not explicitly stated in article titles or keywords. These approaches are unable to perform semantic searches and contextual understanding, limiting their effectiveness in classifying topics and characterizing studies. In this paper, we address these limitations by leveraging Generative AI models, specifically transformers and Retrieval-Augmented Generation (RAG), to automate and enhance bibliometric analysis. We developed a technical workflow that integrates a vector database, Sentence Transformers, a Gaussian Mixture Model (GMM), Retrieval Agent, and Large Language Models (LLMs) to enable contextual search, topic ranking, and characterization of research using customized prompt templates. A pilot study analyzing 223 urban science-related articles published in Nature Communications over the past decade highlights the effectiveness of our approach in generating insightful summary statistics on the quality, scope, and characteristics of papers in high-impact journals. This study introduces a new paradigm for enhancing bibliometric analysis and knowledge retrieval in urban research, positioning an AI agent as a powerful tool for advancing research evaluation and understanding.
Reflections on Disentanglement and the Latent Space
Venue: arXiv cs.CY 2024
Year: 2024

The latent space of image generative models is a multi-dimensional space of compressed hidden visual knowledge. Its entity captivates computer scientists, digital artists, and media scholars alike. Latent space has become an aesthetic category in AI art, inspiring artistic techniques such as the latent space walk, exemplified by the works of Mario Klingemann and others. It is also viewed as cultural snapshots, encoding rich representations of our visual world. This paper proposes a double view of the latent space, as a multi-dimensional archive of culture and as a multi-dimensional space of potentiality. The paper discusses disentanglement as a method to elucidate the double nature of the space and as an interpretative direction to exploit its organization in human terms. The paper compares the role of disentanglement as potentiality to that of conditioning, as imagination, and confronts this interpretation with the philosophy of Deleuzian potentiality and Hume's imagination. Lastly, this paper notes the difference between traditional generative models and recent architectures.
Recent advancements in LLM Red-Teaming: Techniques, Defenses, and Ethical Considerations
Venue: arXiv cs.CL 2024
Year: 2024

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language processing tasks, but their vulnerability to jailbreak attacks poses significant security risks. This survey paper presents a comprehensive analysis of recent advancements in attack strategies and defense mechanisms within the field of Large Language Model (LLM) red-teaming. We analyze various attack methods, including gradient-based optimization, reinforcement learning, and prompt engineering approaches. We discuss the implications of these attacks on LLM safety and the need for improved defense mechanisms. This work aims to provide a thorough understanding of the current landscape of red-teaming attacks and defenses on LLMs, enabling the development of more secure and reliable language models.
Catastrophic Cyber Capabilities Benchmark (3CB): Robustly Evaluating LLM Agent Cyber Offense Capabilities
Venue: arXiv cs.CR 2024
Year: 2024

LLM agents have the potential to revolutionize defensive cyber operations, but their offensive capabilities are not yet fully understood. To prepare for emerging threats, model developers and governments are evaluating the cyber capabilities of foundation models. However, these assessments often lack transparency and a comprehensive focus on offensive capabilities. In response, we introduce the Catastrophic Cyber Capabilities Benchmark (3CB), a novel framework designed to rigorously assess the real-world offensive capabilities of LLM agents. Our evaluation of modern LLMs on 3CB reveals that frontier models, such as GPT-4o and Claude 3.5 Sonnet, can perform offensive tasks such as reconnaissance and exploitation across domains ranging from binary analysis to web technologies. Conversely, smaller open-source models exhibit limited offensive capabilities. Our software solution and the corresponding benchmark provides a critical tool to reduce the gap between rapidly improving capabilities and robustness of cyber offense evaluations, aiding in the safer deployment and regulation of these powerful technologies.
TIGER: Temporally Improved Graph Entity Linker
Venue: arXiv cs.LG 2024
Year: 2024

Knowledge graphs change over time, for example, when new entities are introduced or entity descriptions change. This impacts the performance of entity linking, a key task in many uses of knowledge graphs such as web search and recommendation. Specifically, entity linking models exhibit temporal degradation - their performance decreases the further a knowledge graph moves from its original state on which an entity linking model was trained. To tackle this challenge, we introduce \textbf{TIGER}: a \textbf{T}emporally \textbf{I}mproved \textbf{G}raph \textbf{E}ntity Linke\textbf{r}. By incorporating structural information between entities into the model, we enhance the learned representation, making entities more distinguishable over time. The core idea is to integrate graph-based information into text-based information, from which both distinct and shared embeddings are based on an entity's feature and structural relationships and their interaction. Experiments on three datasets show that our model can effectively prevent temporal degradation, demonstrating a 16.24\% performance boost over the state-of-the-art in a temporal setting when the time gap is one year and an improvement to 20.93\% as the gap expands to three years. The code and data are made available at \url{https://github.com/pengyu-zhang/TIGER-Temporally-Improved-Graph-Entity-Linker}.
"ChatGPT, Don't Tell Me What to Do": Designing AI for Context Analysis in Humanitarian Frontline Negotiations
Venue: arXiv cs.HC 2024
Year: 2024

Frontline humanitarian negotiators are increasingly exploring ways to use AI tools in their workflows. However, current AI-tools in negotiation primarily focus on outcomes, neglecting crucial aspects of the negotiation process. Through iterative co-design with experienced frontline negotiators (n=32), we found that flexible tools that enable contextualizing cases and exploring options (with associated risks) are more effective than those providing direct recommendations of negotiation strategies. Surprisingly, negotiators demonstrated tolerance for occasional hallucinations and biases of AI. Our findings suggest that the design of AI-assisted negotiation tools should build on practitioners' existing practices, such as weighing different compromises and validating information with peers. This approach leverages negotiators' expertise while enhancing their decision-making capabilities. We call for technologists to learn from and collaborate closely with frontline negotiators, applying these insights to future AI designs and jointly developing professional guidelines for AI use in humanitarian negotiations.
RealEra: Semantic-level Concept Erasure via Neighbor-Concept Mining
Venue: arXiv cs.CV 2024
Year: 2024

The remarkable development of text-to-image generation models has raised notable security concerns, such as the infringement of portrait rights and the generation of inappropriate content. Concept erasure has been proposed to remove the model's knowledge about protected and inappropriate concepts. Although many methods have tried to balance the efficacy (erasing target concepts) and specificity (retaining irrelevant concepts), they can still generate abundant erasure concepts under the steering of semantically related inputs. In this work, we propose RealEra to address this "concept residue" issue. Specifically, we first introduce the mechanism of neighbor-concept mining, digging out the associated concepts by adding random perturbation into the embedding of erasure concept, thus expanding the erasing range and eliminating the generations even through associated concept inputs. Furthermore, to mitigate the negative impact on the generation of irrelevant concepts caused by the expansion of erasure scope, RealEra preserves the specificity through the beyond-concept regularization. This makes irrelevant concepts maintain their corresponding spatial position, thereby preserving their normal generation performance. We also employ the closed-form solution to optimize weights of U-Net for the cross-attention alignment, as well as the prediction noise alignment with the LoRA module. Extensive experiments on multiple benchmarks demonstrate that RealEra outperforms previous concept erasing methods in terms of superior erasing efficacy, specificity, and generality. More details are available on our project page https://realerasing.github.io/RealEra/ .
ACER: Automatic Language Model Context Extension via Retrieval
Venue: arXiv cs.CL 2024
Year: 2024

Long-context modeling is one of the critical capabilities of language AI for digesting and reasoning over complex information pieces. In practice, long-context capabilities are typically built into a pre-trained language model~(LM) through a carefully designed context extension stage, with the goal of producing generalist long-context capabilities. In our preliminary experiments, however, we discovered that the current open-weight generalist long-context models are still lacking in practical long-context processing tasks. While this means perfectly effective long-context modeling demands task-specific data, the cost can be prohibitive. In this paper, we draw inspiration from how humans process a large body of information: a lossy \textbf{retrieval} stage ranks a large set of documents while the reader ends up reading deeply only the top candidates. We build an \textbf{automatic} data synthesis pipeline that mimics this process using short-context LMs. The short-context LMs are further tuned using these self-generated data to obtain task-specific long-context capabilities. Similar to how pre-training learns from imperfect data, we hypothesize and further demonstrate that the short-context model can bootstrap over the synthetic data, outperforming not only long-context generalist models but also the retrieval and read pipeline used to synthesize the training data in real-world tasks such as long-context retrieval augmented generation.